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formatting RAxML trees in newick utilities #4

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siriusb-nox opened this issue Jun 26, 2018 · 0 comments
Open

formatting RAxML trees in newick utilities #4

siriusb-nox opened this issue Jun 26, 2018 · 0 comments

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@siriusb-nox
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Dear Prof. Mirarab,

I am trying to use DiscoVista in a set of 291 gene trees (to see support of my clades along genes). After sucessfully creating all directories required by DiscoVista, I came across this issue:
"dendropy.dataio.newickreader.NewickReaderMalformedStatementError: Error parsing data source '/data/RAxML_unroot/genetrees/5716/5716-FNA/estimated_gene_trees.tree' on line 1 at column 7: Expecting ':', ')', ',' or ';' after reading label but found 'C-naudinianus'"

I thought RAxML bipartition files were following the format you requested, but it seems it is not the case. Do you have perhaps at hand the command reuired in newick utilities to reformat the trees and make them fit to DiscoVista (I wnt through the manual but could not find a command to draw support on branches)?

Thank you in advance for any help!

Best,

Oscar

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